Metadata-Version: 2.1
Name: spamosaic
Version: 1.0.0
Summary: SpaMosaic: mosaic integration of spatial multi-omics with GNN and contrastive learning
Home-page: https://github.com/JinmiaoChenLab/SpaMosaic
Author: Jinmiao Lab
Author-email: contact@jinmiaolab.org
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: anndata==0.12.1
Requires-Dist: annoy==1.17.3
Requires-Dist: h5py==3.10.0
Requires-Dist: harmony-pytorch==0.1.7
Requires-Dist: hnswlib==0.8.0
Requires-Dist: matplotlib==3.7.4
Requires-Dist: networkx==3.1
Requires-Dist: numpy==1.22.4
Requires-Dist: pandas==1.5.3
Requires-Dist: PyYAML==6.0.2
Requires-Dist: scanpy==1.11.4
Requires-Dist: scikit-learn==1.3.2
Requires-Dist: scipy==1.16.1
Requires-Dist: seaborn==0.13.2
Requires-Dist: torch==2.0.0
Requires-Dist: torch-geometric==2.6.1
Requires-Dist: torch-scatter==2.1.2
Requires-Dist: torch-sparse==0.6.18
Requires-Dist: tqdm==4.66.1

# SpaMosaic

**SpaMosaic** is a Python package for spatial multi-omics data integration using contrastive learning and graph neural networks. It supports integration of partially overlapping modalities and facilitates downstream analyses such as spatial domain identification and modality imputation.

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## 🔧 Features

- **Horizontal integration**: integrates multiple slices within a single modality
- **Vertical integration**: integrates multiple modalities measured from the same slice
- **Mosaic integration**: integrates multiple slices with overallping modalities 
- **Imputation**: imputes expression profiles of missing omics

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## 🚀 Installation

We recommend using Python 3.8+ and a Conda environment:

```bash
pip install spamosaic
```

## 📚 Documentation
📖 Full tutorials and API reference:
👉 https://spamosaic.readthedocs.io

## 📄 License
SpaMosaic is released under the MIT License.
© 2025 Jinmiao Lab
